NatureBench/docker/Dockerfile.base at main · FrontisAI/NatureBench · GitHub

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# ==============================================================================
# NatureBench base image for ML task containers
# ==============================================================================
# Build:  docker build -t naturebench-base:v3 -f Dockerfile.base .
# ==============================================================================
# Release base image notes:
#   - CUDA 12.6 → 11.8 for broader host-driver compatibility
#   - PyTorch index-url cu126 → cu118 while keeping torch 2.6.0
#   - numpy pinned to 1.26.4 (torch cu118 wheels require numpy<2.0)
#   - All pip packages remain pinned for reproducibility
# ==============================================================================

FROM nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04

SHELL ["/bin/bash", "-o", "pipefail", "-c"]

ENV DEBIAN_FRONTEND=noninteractive \
    PIP_NO_CACHE_DIR=1 \
    PIP_DISABLE_PIP_VERSION_CHECK=1 \
    PYTHONDONTWRITEBYTECODE=1 \
    PYTHONUNBUFFERED=1

# This base image is shared by many task images, so it should cover the common
# scientific Python stack while avoiding heavyweight or fast-moving frameworks
# that frequently break dependency resolution. Task-specific images can add
# TensorFlow, JAX, Scanpy, or any other specialized packages as needed.

# ── System dependencies + Python 3.11 ────────────────────────────────────────
RUN apt-get update \
    && apt-get install -y --no-install-recommends \
    software-properties-common \
    build-essential \
    cmake \
    gfortran \
    git \
    wget \
    curl \
    unzip \
    zip \
    vim \
    swig \
    libffi-dev \
    libssl-dev \
    libhdf5-dev \
    libopenblas-dev \
    libsm6 \
    libxext6 \
    libgl1 \
    libglib2.0-0 \
    ffmpeg \
    && add-apt-repository ppa:deadsnakes/ppa -y \
    && apt-get update \
    && apt-get install -y --no-install-recommends \
    python3.11 \
    python3.11-dev \
    python3.11-venv \
    && rm -rf /var/lib/apt/lists/*

# Keep Ubuntu's system python3 untouched for OS tooling like apt, but put an
# isolated Python 3.11 environment first on PATH for solver code.
RUN python3.11 -m venv /opt/py311 \
    && /opt/py311/bin/python -m pip install --upgrade pip setuptools wheel

ENV VIRTUAL_ENV=/opt/py311 \
    PATH="/opt/py311/bin:${PATH}"

# ── Core Scientific Computing ────────────────────────────────────────────────
RUN python -m pip install \
    numpy==1.26.4 \
    scipy==1.14.1 \
    pandas==2.2.3 \
    matplotlib==3.10.0 \
    seaborn==0.13.2 \
    h5py==3.12.1 \
    tables==3.10.1 \
    pyarrow==18.1.0 \
    networkx==3.4.2 \
    igraph==0.11.8 \
    sympy==1.13.1 \
    statsmodels==0.14.4 \
    scikit-image==0.24.0 \
    opencv-python-headless==4.11.0.86 \
    Pillow==11.1.0 \
    tqdm==4.67.1 \
    rich==13.9.4 \
    jupyter==1.1.1

# ── ML Frameworks ────────────────────────────────────────────────────────────
RUN python -m pip install \
    torch==2.6.0 \
    torchvision==0.21.0 \
    torchaudio==2.6.0 \
    --index-url https://download.pytorch.org/whl/cu118

RUN python -m pip install \
    scikit-learn==1.6.1 \
    xgboost==2.1.3 \
    lightgbm==4.5.0 \
    catboost==1.2.7

# ── Deep Learning Ecosystem ──────────────────────────────────────────────────
RUN python -m pip install \
    transformers==4.48.1 \
    datasets==3.2.0 \
    tokenizers==0.21.0 \
    lightning==2.5.0 \
    einops==0.8.0 \
    timm==1.0.12 \
    accelerate==1.3.0 \
    optuna==4.2.0 \
    safetensors==0.5.2 \
    sentencepiece==0.2.0 \
    wandb==0.19.1

# ── Domain Libraries ─────────────────────────────────────────────────────────
RUN python -m pip install \
    anndata==0.11.3 \
    biopython==1.85 \
    rdkit==2024.9.6 \
    ase==3.23.0 \
    pymatgen==2024.11.13 \
    nibabel==5.3.2 \
    nilearn==0.11.1

# ── Node.js + Agent CLIs (Claude Code, Codex, Gemini) ──────────────────────
RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
    && apt-get install -y --no-install-recommends nodejs \
    && rm -rf /var/lib/apt/lists/* \
    && npm install -g @anthropic-ai/claude-code @openai/codex @google/gemini-cli

# ── Cleanup ──────────────────────────────────────────────────────────────────
ENV DEBIAN_FRONTEND=
WORKDIR /home